FAQ
Contents
- How do I log in to Njord?
- How do I change my password?
- How do I compile my software with MPI?
- How do I compile thread-based software?
- How do I compile my OpenMP software?
- How do I change the compiler?
- How do I see all the flags that my software is compiled with?
- My text contains ^M characters and I get an error when I use the text.
- How do I see how much wall time a job has used?
- How do I see how much memory my program uses while running in batch?
- How do I kill a job?
- I don't have enough disk quota to run my job. What shall I do?
- How do I check how many hour that I have left on my project account?
- How do I speed up file compression by utilizing available cores on a multi-core node?
- My problem is not listed here. What do I do?
How do I log in to Njord?
To log in to Njord you will need an ssh client. The syntax for logging in depends on the ssh client that you use. From Linux it is sufficient to open a terminal and type "ssh username@njord.hpc.ntnu.no". If your user name on your Linux desktop is the same as your user name on Njord, then you only need to type "ssh njord.hpc.ntnu.no". See also Log in with SSH.
Njord is only available for login from the Norwegian academic networks. We do not open up for access from private ISP's. However, collaborating researchers might be able to log directly into the system if submitting relevant IP numbers in a support case.
How do I change my password?
Log in to this web page to change password on njord: https://www.metacenter.no/user/
How do I compile my software with MPI?
Compile your program with one of the system MPI compilers: mpxlf, mpxlf90, mpxlf95, mpcc, or mpCC. See also Compilers, Libraries and Tools.
How do I compile thread-based software?
If you are compiling software that uses threads, but not MPI, then you must use one of the compilers with an added _r: xlf_r, xlf90_r, xlf95_r, xlc_r, or xlc++_r. If your program also uses MPI then you can choose between the standard MPI compilers and the compilers with an added _r: mpxlf_r, mpxlf90_r, mpxlf95_r, mpcc_r, or mpCC_r. Both sets of compilers are thread-safe. See also Compilers, Libraries and Tools.
How do I compile my OpenMP software?
Compile your program with compiler option: -qsmp=omp for the Fortran and c compiler (xlf90_r and xlc_r). For the GNU compiler use option -fopenmp, eg. gcc -fopenmp -o helloworld helloworld.c. See also The GCC Compiler Suite.
How do I change the compiler?
If your program is written in C or C++ then you can use the GCC 4.4.3 compiler on Njord by compiling your program with either gcc or g++. If your program is written in Fortran then you must use one of the system compilers, as gfortran is not available on Njord. See also The GCC Compiler Suite.
How do I see all the flags that my software is compiled with?
Add -v to the list of compiler flags. This works both with the system compilers and with GNU's C and C++ compilers.
My text contains ^M characters and I get an error when I use the text.
An example of such an error is:
/bin/ksh^M: bad interpreter
You have created a text file in the Windows text format. You must either store your file in the UNIX text format, convert the text file to the UNIX text format during transmission to Njord or later on convert the text file on Njord.
Use the dox2unix command to convert the text file on Njord, e.g.:
$ dos2unix myrun.job
How do I see how much wall time a job has used?
List the resource consumption for your job with llq, like this:
$ llq -x -j f02n02io.539131.0 Id Owner Submitted ST PRI Class Running on Job CPU ----------------- --------- ----------- -- --- -------- ---------- ------------- f02n02io.539131.0 ersland 8/9 13:12 R 50 large f08n01 440+01:28:40
The "Job CPU" column shows the total number of CPU-hours used by the job so far. Divide this number by the number of CPUs (=number-of-nodes X 16) you are using, and you get the wall time of your job.
How do I see how much memory my program uses while running in batch?
Type:
$ llq
Locate the job Id to the left on the list and then type:
$ llq -w «job id»
Locate the "high water" number in the "Real Memory" section. This gives you the max. number of 4KB pages that your program has used until now, so you must multiply this number by 4 to convert it to KB.
Doing this interactively can e.g. help you check whether your program leaks memory, but you can also make your job script produce this information at completion. In this case, you must add the following line at the end of your job script:
llq -w $LOADL_STEP_ID
How do I kill a job?
In order to kill a job that you have submitted to the batch system, you must first find the job id with the "llq" command, e.g.:
$ llq ... f05n02io.622574.0 hrn 10/4 10:31 I 50 express ...
Then you cancel the job by issuing the order "llcancel «job id»", e.g.:
$ llcancel f05n02io.622574.0
I don't have enough disk quota to run my job. What shall I do?
You can as default store up to 20 GiB of data in your home directory before you get an automatic warning from Njord and if you reach 40 GiB then you will be unable to continue working, but you can create a directory in /work, with the same name as your user name, in which you can store up to 500 GiB.
In contrast to your home directory, which is backed up regularly, directories under /work are never backed up and files there that are older than 21 days are deleted automatically. /work should also be slightly faster than your home directory and is therefore ideal for storing the temporary files that your program produces, but the final results must be copied to your home directory when your program is finished. See also File Systems.
If the above mentioned limits are insufficient for you, then you can contact support at NTNU (support-ntnu@notur.no) and ask for an increase of your disk quota.
How do I check how many hours that I have left on my project account?
Type:
$ cost
Locate the account name on the output and then type:
$ cost -k «account name»
How do I speed up file compression by utilizing available cores on a multi-core node?
The number of files that it is possible to create on a UNIX computer such as Njord is restricted, because of problems with administering the meta-data associated with each file. Njord has, however, large disks as well as a parallel file system, allowing users to have a large amount of data in each file. Programs that run on Njord should therefore create few, but large files.
Since data usually is binary and Njord has large disks it is normally not advisable to compress files on Njord. If you need to package your files together, then do so with the tar command without compressing the files, e.g.:
tar cvf foo.tar *.cc *.h
However, if you absolutely must compress your files, then you can read this page and then submit a job to batch that performs the compression in parallel.
My problem is not listed here. What do I do?
See whether your question is covered in the Njord User Guide. If not, then send an email to our administrators at support (support-ntnu@notur.no) describing your problem. It will be beneficial to provide the job number which failed, and paths to output file, error file, submit script and Makefile. Then one of the engineers will help you as soon as possible.
